On Tue, 27 Oct 2020 at 21:36, zimoun <zimon.touto...@gmail.com> wrote:
On part of the story,
> --8<---------------cut here---------------start------------->8---
> (define-public r-diffcyt
> (package
> (name "r-diffcyt")
[...]
> (native-inputs
`(("r-knitr" ,r-knitr)
("r-rmarkdown" ,r-rmarkdown)
("pandoc" ,pandoc)
("pandoc" ,pandoc-citeproc)
("r-biocstyle" ,r-biocstyle)))
[...]
> (license expat)))
> --8<---------------cut here---------------end--------------->8---
leads to:
--8<---------------cut here---------------start------------->8---
starting phase `check'
Testing examples for package ‘diffcyt’
Running specific tests for package ‘diffcyt’
Running ‘testthat.R’
Running vignettes for package ‘diffcyt’
Running ‘diffcyt_workflow.Rmd’
*** Source Errors ***
File diffcyt_workflow.R:
Cannot find the file(s): "diffcyt.png"
*** Weave Errors ***
File diffcyt_workflow.Rmd:
Cannot find the file(s): "diffcyt.png"
--8<---------------cut here---------------end--------------->8---
and I have no clue what I am missing.
The other part of the story is:
--8<---------------cut here---------------start------------->8---
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'delete
(lambda _
(delete-file-recursively "inst")
#t)))))
--8<---------------cut here---------------end--------------->8---
leads to:
--8<---------------cut here---------------start------------->8---
starting phase `install'
* installing *source* package ‘diffcyt’ ...
** using staged installation
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file
'/gnu/store/nqymkk1g0zsmf2wwrq5zd6rh7sdhvpjm-r-diffcyt-1.8.8/site-library/00LOCK-diffcyt/00new/diffcyt/doc/index.html':
No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing
‘/gnu/store/nqymkk1g0zsmf2wwrq5zd6rh7sdhvpjm-r-diffcyt-1.8.8/site-library/diffcyt’
command "R" "CMD" "INSTALL" "--install-tests"
"--library=/gnu/store/nqymkk1g0zsmf2wwrq5zd6rh7sdhvpjm-r-diffcyt-1.8.8/site-library/"
"--built-timestamp=1970-01-01" "." failed with status 1
builder for `/gnu/store/9dwqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv'
failed with exit code 1
build of /gnu/store/9dwqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv failed
View build log at
'/var/log/guix/drvs/9d/wqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv.bz2'.
guix build: error: build of
`/gnu/store/9dwqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv' failed
--8<---------------cut here---------------end--------------->8---
and the addition of ’(mkdir-p "inst/doc")’ makes the build pass, but:
file:///gnu/store/…-r-diffcyt-1.8.8/site-library/diffcyt/doc/index.html
shows one HTML link pointing to:
file:///gnu/store/…-r-diffcyt-1.8.8/library/diffcyt/doc/diffcyt_workflow.html
which does not exist.
Another random example is ’r-ebimage’,
--8<---------------cut here---------------start------------->8---
$ tar xvf $(guix build r-ebimage -S) | grep "inst/doc"
EBImage/inst/doc/
EBImage/inst/doc/EBImage-introduction.R
EBImage/inst/doc/EBImage-introduction.Rmd
EBImage/inst/doc/EBImage-introduction.html
$ md5sum EBImage/inst/doc/EBImage-introduction.html $(guix build
r-ebimage)/site-library/EBImage/doc/EBImage-introduction.html
4dabd489660ff7909e4787cb23fe89d7 EBImage/inst/doc/EBImage-introduction.html
4dabd489660ff7909e4787cb23fe89d7
/gnu/store/9lmzhb0palxsm8ynacy2nnh5w8gvbn6j-r-ebimage-4.30.0/site-library/EBImage/doc/EBImage-introduction.html
--8<---------------cut here---------------end--------------->8---
Well bit-to-bit identical HTML as upstream… strong evidence that the
documentation is not locally generated. And the upstream-upstream
https://github.com/aoles/EBImage/tree/master/inst
does not contains this HTML, AFAICT.
BTW, going via the Source Repository
git clone https://git.bioconductor.org/packages/EBImage
i.e., ’git-fetch’ instead of ’url-fetch’ seems the right direction to
fix. Because:
1. it is the “real” source and this source is easily verifiable; for
example it is easy to check the commit hash of the Bioconductor repo
against the one of the upstream GitHub repo.
2. the fallback to SWH works for git-fetch. The tarball is not ready
yet; and who knows when… :-)
All the best,
simon
